Abstract FreeSurfer is a tool for the analysis of Magnetic Resonance Imaging (MRI) that has proven to be a flexible and powerful technology for quantifying the effects of many conditions, including numerous neurological disorders, on human brain anatomy, connectivity, vasculature, chemical composition, physiology and function. In the past 20 years, these open source tools have been developed to accurately and automatically segment an array of brain structures. In this project, we seek the resources to radically increase the speed, accuracy and flexibility of these tools, taking advantage of exciting new results in Deep Learning. This will enable us to more accurately quantify neuroanatomical changes that are critical to diagnosing, staging and assessing the efficacy of potential therapeutic interventions in diseases such as Alzheimer?s and Parkinson?s. This includes the generation of documentation, tutorials, unit tests, regression tests and system tests to harden the tools and make them usable by clinicians and neuroscientists, and finally the distribution and support of the data, manual labelings and tools to the more than 35,000 researchers that use FreeSurfer through our existing open source mechanism.